added homova command

[mothur.git] / nast.cpp

diff --git a/nast.cpp b/nast.cpp
index 9cdf1b26619a170b7f7d67cc9edc60d89d66559a..28cc659e9c5a6090bcd6cb5edecdc7cf9d6c9ec0 100644 (file)
--- a/nast.cpp
+++ b/nast.cpp
@@ -25,8 +25,10 @@ Nast::Nast(Alignment* method, Sequence* cand, Sequence* temp) : alignment(method
        try {
                m = MothurOut::getInstance();
                maxInsertLength = 0;
+       
                pairwiseAlignSeqs();    //      This is part A in Fig. 2 of DeSantis et al.
                regapSequences();               //      This is parts B-F in Fig. 2 of DeSantis et al.
+               
        }
        catch(exception& e) {
                m->errorOut(e, "Nast", "Nast");
@@ -223,7 +225,7 @@ void Nast::removeExtraGaps(string& candAln, string tempAln, string newTemplateAl
 
 void Nast::regapSequences(){   //This is essentially part B in Fig 2. of DeSantis et al.
        try { 
-       
+       //cout << candidateSeq->getName() << endl;
                string candPair = candidateSeq->getPairwise();
                string candAln = "";
                
@@ -252,6 +254,7 @@ void Nast::regapSequences(){        //This is essentially part B in Fig 2. of DeSantis
                string lastLoop = "";
                
                while(pairwiseAlignIndex<pairwiseLength){
+       //cout << pairwiseAlignIndex << '\t' << fullAlignIndex << '\t' << pairwiseLength << endl;
                        if(isalpha(tempPair[pairwiseAlignIndex]) && isalpha(tempAln[fullAlignIndex])
                           && isalpha(candPair[pairwiseAlignIndex])){
                                //  the template and candidate pairwise and template aligned have characters
@@ -358,6 +361,7 @@ void Nast::regapSequences(){        //This is essentially part B in Fig 2. of DeSantis
                }                                                                                               //      2 of Desantis et al.
 
                candidateSeq->setAligned(candAln);
+       //cout << "here" << endl;
        }
        catch(exception& e) {
                m->errorOut(e, "Nast", "regapSequences");